4MIC
Crystal structure of Gpb in complex with SUGAR (N-{(2E)-3-[4-(PROPAN-2-YL)PHENYL]PROP-2-ENOYL}-BETA-D-GLUCOPYRANOSYLAMINE) (S6)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3SYM | pdb entry 3SYM |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | SMALL TUBES | 6.7 | 289 | 10 mM BES buffer, pH 6.7, SMALL TUBES, temperature 289K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.59 | 52.48 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 128.74 | α = 90 |
b = 128.74 | β = 90 |
c = 116.71 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 43 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 293 | CCD | AGILENT ATLAS CCD | 2013-02-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | OXFORD DIFFRACTION ENHANCE ULTRA | 1.5419 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2.45 | 18.23 | 91.4 | 0.099 | 6.3 | 2.2 | 33056 | 33056 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.45 | 2.58 | 95.6 | 0.531 | 1.8 | 2.2 | 4997 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | pdb entry 3SYM | 2.45 | 18.14 | 31316 | 31316 | 1646 | 89.96 | 0.18899 | 0.18663 | 0.23354 | RANDOM | 36.423 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.72 | 0.72 | -1.44 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.868 |
r_dihedral_angle_4_deg | 17.8 |
r_dihedral_angle_3_deg | 15.392 |
r_dihedral_angle_1_deg | 5.393 |
r_angle_refined_deg | 0.981 |
r_angle_other_deg | 0.74 |
r_chiral_restr | 0.057 |
r_bond_refined_d | 0.005 |
r_gen_planes_refined | 0.003 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6577 |
Nucleic Acid Atoms | |
Solvent Atoms | 113 |
Heterogen Atoms | 25 |
Software
Software | |
---|---|
Software Name | Purpose |
CrysalisPro | data collection |
REFMAC | refinement |
CrysalisPro | data reduction |
SCALA | data scaling |
REFMAC | phasing |